FBX Converter from the Mac terminal?
You won't get any help using the Autodesk converter here, but if you are asking whether you can use blender to do the conversions, then the answer might be yes. Blender is able to import and export both obj and fbx files, you will need to do some tests to see if the models you have are handled correctly.

Blender has a python interpreter built into it, you can use blender's python console to enter python commands to do your conversion. You can also open a text file in blender's text editor and run it as a python script.

You could also start blender in the terminal and have it act as an interactive python console in the terminal without using blender's gui.

The commands you want to use to convert your models are bpy.ops.import_scene.obj() and bpy.ops.export_scene.fbx()

You could start with a script like 

import bpy
import os

src_dir = '/Users/name/Desktop/obj_files'
dest_dir = '/Users/name/Desktop/fbx_files'

for f in os.listdir(src_dir):
    # delete all existing objects
    bpy.ops.object.select_all(action='SELECT')
    bpy.ops.object.delete()
    bpy.ops.import_scene.obj(filepath=os.path.join(src_dir,f))
    bpy.ops.export_scene.fbx(filepath=os.path.join(dest_dir,f))